Hi,
<: means “residues within” so if _any_ part of the residue meets the
distance cutoff the whole residue is selected. Try <@ (atoms within)
instead.
-Dan
On Thu, Jul 9, 2020 at 8:05 PM Kenneth Huang <kennethneltharion.gmail.com>
wrote:
> Hi all,
>
> I'm running into an odd situation where the behavior of the mask command
> doesn't seem to be lining up exactly with the actual measured distance, ie
> if I have
>
> mask "(:35.N4<:5.5)&:47-135&( :LYS.NZ | :ARG.NH1,NH2 | :GLU.OE1,OE2 |
> > :ASP.OD1,OD2 )" maskout maskout_N4.dat
> >
>
> To measure any charged groups of the protein within 5.5 A of the N4 group
> on a DNA base, it says frame 1 has both NH groups on an ARG within the
> raidus,
>
> #Frame AtomNum Atom ResNum Res MolNum
> > 1 2527 NH1 108 ARG 3
> > 1 2530 NH2 108 ARG 3
> >
>
> But when I try to fetch the distance via
>
> distance dN4 :35.N4 :108.NH1 out dist.m35N4-108.dat noimage
> > distance dN4b :35.N4 :108.NH2 out dist.m35N4b-108.dat noimage
> >
>
> The distance I get for both sets say that it's mugh further than the 5.5
> radius of mask?
>
> 1 6.4996
> >
> >
> 1 5.7482
> >
> >
> My first thought is I've somehow messed up the selection algebra in the
> mask portion, but I can't seem to find an actual error in it?
>
> Best,
>
> Kenneth
>
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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Received on Thu Jul 09 2020 - 19:30:04 PDT
